Only suggest Seurat; check if it's installed in the as.Seurat() function

LieberInstitute · Oct 14, 2024 · ea7164f · ea7164f
1 parent c7c9552
commit ea7164f
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,6 +38,7 @@ Suggests:
     RefManageR,
     rmarkdown,
     sessioninfo,
+    Seurat,
     SingleCellExperiment,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
@@ -54,7 +55,6 @@ Imports:
     readr,
     rjson,
     S4Vectors,
-    Seurat,
     spatialLIBD (>= 1.17.8),
     stringr,
     SummarizedExperiment,

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,6 +14,7 @@ import(SpatialExperiment)
 import(dplyr)
 import(spatialLIBD)
 import(xml2)
+importFrom(BiocBaseUtils,checkInstalled)
 importFrom(BiocGenerics,cbind)
 importFrom(Matrix,Matrix)
 importFrom(S4Vectors,DataFrame)

diff --git a/R/as.Seurat.R b/R/as.Seurat.R
@@ -27,6 +27,7 @@
 #' @importFrom SummarizedExperiment colData
 #' @importFrom grDevices col2rgb
 #' @importFrom methods new
+#' @importFrom BiocBaseUtils checkInstalled
 #'
 #' @examples
 #' ## Download some example data
@@ -59,6 +60,9 @@ as.Seurat <- function(
             "imagecol" = "pxl_col_in_fullres"
         ),
         verbose = TRUE) {
+    #   Seurat is only suggested
+    BiocBaseUtils::checkInstalled('Seurat')
+
     SPOT_DIAMETER <- 55e-6
 
     #   Ensure all necessary columns are present in colData